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1.
Nucleic Acids Res ; 51(15): 7972-7987, 2023 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-37395399

RESUMO

DNA-dependent protein kinase (DNA-PK) plays a critical role in non-homologous end joining (NHEJ), the predominant pathway that repairs DNA double-strand breaks (DSB) in response to ionizing radiation (IR) to govern genome integrity. The interaction of the catalytic subunit of DNA-PK (DNA-PKcs) with the Ku70/Ku80 heterodimer on DSBs leads to DNA-PK activation; however, it is not known if upstream signaling events govern this activation. Here, we reveal a regulatory step governing DNA-PK activation by SIRT2 deacetylation, which facilitates DNA-PKcs localization to DSBs and interaction with Ku, thereby promoting DSB repair by NHEJ. SIRT2 deacetylase activity governs cellular resistance to DSB-inducing agents and promotes NHEJ. SIRT2 furthermore interacts with and deacetylates DNA-PKcs in response to IR. SIRT2 deacetylase activity facilitates DNA-PKcs interaction with Ku and localization to DSBs and promotes DNA-PK activation and phosphorylation of downstream NHEJ substrates. Moreover, targeting SIRT2 with AGK2, a SIRT2-specific inhibitor, augments the efficacy of IR in cancer cells and tumors. Our findings define a regulatory step for DNA-PK activation by SIRT2-mediated deacetylation, elucidating a critical upstream signaling event initiating the repair of DSBs by NHEJ. Furthermore, our data suggest that SIRT2 inhibition may be a promising rationale-driven therapeutic strategy for increasing the effectiveness of radiation therapy.


Assuntos
Quebras de DNA de Cadeia Dupla , Proteínas Quinases , DNA/genética , DNA/metabolismo , Reparo do DNA por Junção de Extremidades , Reparo do DNA , Proteína Quinase Ativada por DNA/genética , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Autoantígeno Ku/metabolismo , Proteínas Nucleares/metabolismo , Proteínas Quinases/genética , Sirtuína 2/genética , Sirtuína 2/metabolismo , Humanos
2.
Chem Commun (Camb) ; 56(25): 3685-3688, 2020 Mar 26.
Artigo em Inglês | MEDLINE | ID: mdl-32119023

RESUMO

Fragment antigen-binding domains (Fabs) from anti-Frizzled and anti-LRP6 monoclonal antibodies were conjugated using SpyTag-SpyCatcher chemistry via a one-pot reaction. The resulting synthetic heterodimeric agonist outperformed the natural ligand, Wnt-3a, in activating canonical Wnt signaling in mammalian cells. This approach should be broadly applicable to activate receptor-mediated cellular signaling.


Assuntos
Anticorpos Monoclonais/farmacologia , Proteína Wnt3A/agonistas , Anticorpos Monoclonais/química , Dimerização , Humanos , Ligantes , Estrutura Molecular , Via de Sinalização Wnt/efeitos dos fármacos
3.
J Biol Chem ; 293(13): 4653-4663, 2018 03 30.
Artigo em Inglês | MEDLINE | ID: mdl-29382721

RESUMO

Mechanistic details of intramembrane aspartyl protease (IAP) chemistry, which is central to many biological and pathogenic processes, remain largely obscure. Here, we investigated the in vitro kinetics of a microbial intramembrane aspartyl protease (mIAP) fortuitously acting on the renin substrate angiotensinogen and the C-terminal transmembrane segment of amyloid precursor protein (C100), which is cleaved by the presenilin subunit of γ-secretase, an Alzheimer disease (AD)-associated IAP. mIAP variants with substitutions in active-site and putative substrate-gating residues generally exhibit impaired, but not abolished, activity toward angiotensinogen and retain the predominant cleavage site (His-Thr). The aromatic ring, but not the hydroxyl substituent, within Tyr of the catalytic Tyr-Asp (YD) motif plays a catalytic role, and the hydrolysis reaction incorporates bulk water as in soluble aspartyl proteases. mIAP hydrolyzes the transmembrane region of C100 at two major presenilin cleavage sites, one corresponding to the AD-associated Aß42 peptide (Ala-Thr) and the other to the non-pathogenic Aß48 (Thr-Leu). For the former site, we observed more favorable kinetics in lipid bilayer-mimicking bicelles than in detergent solution, indicating that substrate-lipid and substrate-enzyme interactions both contribute to catalytic rates. High-resolution MS analyses across four substrates support a preference for threonine at the scissile bond. However, results from threonine-scanning mutagenesis of angiotensinogen demonstrate a competing positional preference for cleavage. Our results indicate that IAP cleavage is controlled by both positional and chemical factors, opening up new avenues for selective IAP inhibition for therapeutic interventions.


Assuntos
Proteínas Arqueais , Ácido Aspártico Proteases , Methanomicrobiaceae , Presenilinas , Proteólise , Proteínas Arqueais/química , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Ácido Aspártico Proteases/química , Ácido Aspártico Proteases/genética , Ácido Aspártico Proteases/metabolismo , Methanomicrobiaceae/química , Methanomicrobiaceae/genética , Methanomicrobiaceae/metabolismo , Presenilinas/química , Presenilinas/genética , Presenilinas/metabolismo
4.
Acta Biomater ; 68: 125-136, 2018 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-29292168

RESUMO

Protein delivery is often used in tissue engineering applications to control differentiation processes, but is limited by protein instability and cost. An alternative approach is to control the cellular microenvironment through biomaterial-mediated sequestration of cell-secreted proteins important to differentiation. Thus, we utilized heparin-based microparticles to modulate cellular differentiation via protein sequestration in an in vitro model system of endochondral ossification. Heparin and poly(ethylene-glycol) (PEG; a low-binding material control)-based microparticles were incorporated into ATDC5 cell spheroids or incubated with ATDC5 cells in transwell culture. Reduced differentiation was observed in the heparin microparticle group as compared to PEG and no microparticle-containing groups. To determine if observed changes were due to sequestration of cell-secreted protein, the proteins sequestered by heparin microparticles were analyzed using SDS-PAGE and mass spectrometry. It was found that heparin microparticles bound insulin-like growth factor binding proteins (IGFBP)-3 and 5. When incubated with a small-molecule inhibitor of IGFBPs, NBI 31772, a similar delay in differentiation of ATDC5 cells was observed. These results indicate that heparin microparticles modulated chondrocytic differentiation in this system via sequestration of cell-secreted protein, a technique that could be beneficial in the future as a means to control cellular differentiation processes. STATEMENT OF SIGNIFICANCE: In this work, we present a proof-of-principle set of experiments in which heparin-based microparticles are shown to modulate cellular differentiation through binding of cell-secreted protein. Unlike existing systems that rely on expensive protein with limited half-lives to elicit changes in cellular behavior, this technique focuses on temporal modulation of cell-generated proteins. This technique also provides a biomaterials-based method that can be used to further identify sequestered proteins of interest. Thus, this work indicates that glycosaminoglycan-based biomaterial approaches could be used as substitutes or additions to traditional methods for modulating and identifying the cell-secreted proteins involved in directing cellular behavior.


Assuntos
Diferenciação Celular , Micropartículas Derivadas de Células/metabolismo , Condrócitos/citologia , Proteínas/metabolismo , Animais , Biomarcadores/metabolismo , Linhagem Celular Tumoral , Condrócitos/metabolismo , Condrogênese , Regulação da Expressão Gênica , Heparina/química , Proteína 3 de Ligação a Fator de Crescimento Semelhante à Insulina/antagonistas & inibidores , Proteína 5 de Ligação a Fator de Crescimento Semelhante à Insulina/antagonistas & inibidores , Camundongos , Polietilenoglicóis/química , Esferoides Celulares/citologia , Coloração e Rotulagem
5.
Biochem J ; 473(14): 2165-77, 2016 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-27208174

RESUMO

The presence of latent activities in enzymes is posited to underlie the natural evolution of new catalytic functions. However, the prevalence and extent of such substrate and catalytic ambiguity in evolved enzymes is difficult to address experimentally given the order-of-magnitude difference in the activities for native and, sometimes, promiscuous substrate/s. Further, such latent functions are of special interest when the activities concerned do not fall into the domain of substrate promiscuity. In the present study, we show a special case of such latent enzyme activity by demonstrating the presence of two mechanistically distinct reactions catalysed by the catalytic domain of receptor protein tyrosine phosphatase isoform δ (PTPRδ). The primary catalytic activity involves the hydrolysis of a phosphomonoester bond (C─O─P) with high catalytic efficiency, whereas the secondary activity is the hydrolysis of a glycosidic bond (C─O─C) with poorer catalytic efficiency. This enzyme also displays substrate promiscuity by hydrolysing diester bonds while being highly discriminative for its monoester substrates. To confirm these activities, we also demonstrated their presence on the catalytic domain of protein tyrosine phosphatase Ω (PTPRΩ), a homologue of PTPRδ. Studies on the rate, metal-ion dependence, pH dependence and inhibition of the respective activities showed that they are markedly different. This is the first study that demonstrates a novel sugar hydrolase and diesterase activity for the phosphatase domain (PD) of PTPRδ and PTPRΩ. This work has significant implications for both understanding the evolution of enzymatic activity and the possible physiological role of this new chemistry. Our findings suggest that the genome might harbour a wealth of such alternative latent enzyme activities in the same protein domain that renders our knowledge of metabolic networks incomplete.


Assuntos
Proteínas Tirosina Fosfatases Semelhantes a Receptores/química , Proteínas Tirosina Fosfatases Semelhantes a Receptores/metabolismo , Catálise , Domínio Catalítico , Biologia Computacional , Proteínas Tirosina Fosfatases Semelhantes a Receptores/genética , Eletricidade Estática , Especificidade por Substrato
6.
Genes Dev ; 28(13): 1429-44, 2014 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-24990963

RESUMO

The three EglN prolyl hydroxylases (EglN1, EglN2, and EglN3) regulate the stability of the HIF transcription factor. We recently showed that loss of EglN2, however, also leads to down-regulation of Cyclin D1 and decreased cell proliferation in a HIF-independent manner. Here we report that EglN2 can hydroxylate FOXO3a on two specific prolyl residues in vitro and in vivo. Hydroxylation of these sites prevents the binding of USP9x deubiquitinase, thereby promoting the proteasomal degradation of FOXO3a. FOXO transcription factors can repress Cyclin D1 transcription. Failure to hydroxylate FOXO3a promotes its accumulation in cells, which in turn suppresses Cyclin D1 expression. These findings provide new insights into post-transcriptional control of FOXO3a and provide a new avenue for pharmacologically altering Cyclin D1 activity.


Assuntos
Fatores de Transcrição Forkhead/metabolismo , Regulação Neoplásica da Expressão Gênica , Prolina Dioxigenases do Fator Induzível por Hipóxia/metabolismo , Ubiquitina Tiolesterase/metabolismo , Animais , Linhagem Celular , Células Cultivadas , Ciclina D1/genética , Proteína Forkhead Box O3 , Hidroxilação , Células MCF-7 , Camundongos , Ligação Proteica , Estabilidade Proteica
7.
Mol Cell Proteomics ; 13(5): 1184-97, 2014 May.
Artigo em Inglês | MEDLINE | ID: mdl-24556848

RESUMO

Post-translational modifications of proteins regulate diverse cellular functions, with mounting evidence suggesting that hierarchical cross-talk between distinct modifications may fine-tune cellular responses. For example, in apoptosis, caspases promote cell death via cleavage of key structural and enzymatic proteins that in some instances is inhibited by phosphorylation near the scissile bond. In this study, we systematically investigated how protein phosphorylation affects susceptibility to caspase cleavage using an N-terminomic strategy, namely, a modified terminal amino isotopic labeling of substrates (TAILS) workflow, to identify proteins for which caspase-catalyzed cleavage is modulated by phosphatase treatment. We validated the effects of phosphorylation on three of the identified proteins and found that Yap1 and Golgin-160 exhibit decreased cleavage when phosphorylated, whereas cleavage of MST3 was promoted by phosphorylation. Furthermore, using synthetic peptides we systematically examined the influence of phosphoserine throughout the entirety of caspase-3, -7, and -8 recognition motifs and observed a general inhibitory effect of phosphorylation even at residues considered outside the classical consensus motif. Overall, our work demonstrates a role for phosphorylation in controlling caspase-mediated cleavage and shows that N-terminomic strategies can be tailored to study cross-talk between phosphorylation and proteolysis.


Assuntos
Caspases/química , Caspases/metabolismo , Peptídeos/metabolismo , Proteômica/métodos , Células HeLa , Humanos , Marcação por Isótopo , Proteínas de Membrana/metabolismo , Modelos Moleculares , Fosfoproteínas/metabolismo , Fosforilação , Processamento de Proteína Pós-Traducional , Proteínas Serina-Treonina Quinases/metabolismo , Proteólise
8.
Mol Cell ; 51(4): 531-8, 2013 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-23954348

RESUMO

In response to environmental stress, cells often generate pH signals that serve to protect vital cellular components and reprogram gene expression for survival. A major barrier to our understanding of this process has been the identification of signaling proteins that detect changes in intracellular pH. To identify candidate pH sensors, we developed a computer algorithm that searches proteins for networks of proton-binding sidechains. This analysis indicates that Gα subunits, the principal transducers of G protein-coupled receptor (GPCR) signals, are pH sensors. Our structure-based calculations and biophysical investigations reveal that Gα subunits contain networks of pH-sensing sidechains buried between their Ras and helical domains. Further, we show that proton binding induces changes in conformation that promote Gα phosphorylation and suppress receptor-initiated signaling. Together, our computational, biophysical, and cellular analyses reveal an unexpected function for G proteins as mediators of stress-response signaling.


Assuntos
Algoritmos , Subunidades alfa de Proteínas de Ligação ao GTP/química , Prótons , Receptores Acoplados a Proteínas G/metabolismo , Sistemas do Segundo Mensageiro , Estresse Fisiológico , Subunidades alfa de Proteínas de Ligação ao GTP/metabolismo , Guanosina 5'-O-(3-Tiotrifosfato)/metabolismo , Humanos , Concentração de Íons de Hidrogênio , Fosforilação , Ligação Proteica , Estrutura Terciária de Proteína , Transdução de Sinais , Temperatura
9.
PLoS One ; 8(6): e66755, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23826126

RESUMO

Protein kinases play key roles in oncogenic signaling and are a major focus in the development of targeted cancer therapies. Imatinib, a BCR-Abl tyrosine kinase inhibitor, is a successful front-line treatment for chronic myelogenous leukemia (CML). However, resistance to imatinib may be acquired by BCR-Abl mutations or hyperactivation of Src family kinases such as Lyn. We have used multiplexed kinase inhibitor beads (MIBs) and quantitative mass spectrometry (MS) to compare kinase expression and activity in an imatinib-resistant (MYL-R) and -sensitive (MYL) cell model of CML. Using MIB/MS, expression and activity changes of over 150 kinases were quantitatively measured from various protein kinase families. Statistical analysis of experimental replicates assigned significance to 35 of these kinases, referred to as the MYL-R kinome profile. MIB/MS and immunoblotting confirmed the over-expression and activation of Lyn in MYL-R cells and identified additional kinases with increased (MEK, ERK, IKKα, PKCß, NEK9) or decreased (Abl, Kit, JNK, ATM, Yes) abundance or activity. Inhibiting Lyn with dasatinib or by shRNA-mediated knockdown reduced the phosphorylation of MEK and IKKα. Because MYL-R cells showed elevated NF-κB signaling relative to MYL cells, as demonstrated by increased IκBα and IL-6 mRNA expression, we tested the effects of an IKK inhibitor (BAY 65-1942). MIB/MS and immunoblotting revealed that BAY 65-1942 increased MEK/ERK signaling and that this increase was prevented by co-treatment with a MEK inhibitor (AZD6244). Furthermore, the combined inhibition of MEK and IKKα resulted in reduced IL-6 mRNA expression, synergistic loss of cell viability and increased apoptosis. Thus, MIB/MS analysis identified MEK and IKKα as important downstream targets of Lyn, suggesting that co-targeting these kinases may provide a unique strategy to inhibit Lyn-dependent imatinib-resistant CML. These results demonstrate the utility of MIB/MS as a tool to identify dysregulated kinases and to interrogate kinome dynamics as cells respond to targeted kinase inhibition.


Assuntos
Leucemia/metabolismo , Inibidores de Proteínas Quinases/farmacologia , Benzamidas/farmacologia , Linhagem Celular , Sobrevivência Celular/efeitos dos fármacos , Cromatografia de Afinidade , Dasatinibe , Resistencia a Medicamentos Antineoplásicos/genética , Proteínas de Fusão bcr-abl , Humanos , Mesilato de Imatinib , Immunoblotting , NF-kappa B/genética , NF-kappa B/metabolismo , Piperazinas/farmacologia , Proteínas Tirosina Quinases/genética , Proteínas Tirosina Quinases/metabolismo , Pirimidinas/farmacologia , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Tiazóis/farmacologia , Quinases da Família src/antagonistas & inibidores , Quinases da Família src/genética , Quinases da Família src/metabolismo
10.
Toxicol Sci ; 134(1): 83-91, 2013 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-23570992

RESUMO

The zebrafish (Danio rerio) was used to investigate protein expression in the liver following arsenic exposure. Several disorders have been linked to arsenic exposure, including cancer, diabetes, and cardiovascular disease. The mechanisms of arsenic toxicity are poorly understood. Prior studies have described altered gene expression, inflammation, and mitogenic signaling in acute or chronic exposure models. A proteomic approach was employed to investigate arsenic-induced alteration in the zebrafish liver proteome following a 7-day exposure to 50 ppb sodium arsenite. Over 740 unique proteins were identified, with fewer than 2% showing differential expression. Molecular pathway analysis software identified lipid metabolism and transport as potential molecular targets. Immunoblots were used to confirm protein expression changes, whereas qPCR was employed to investigate gene expression changes. Overall, 25 proteins were differentially expressed in a gender-specific manner, 11 in males and 14 in females. Of these 25, a single protein, hydroxysteroid dehydrogenase like 2, showed decreased expression in both males and females following arsenic exposure. These findings indicate that protein expression is altered following arsenic exposure. The changes presented here seem to be most prevalent in lipid transport and metabolic pathways, suggesting a potential increase in fibrosis in males and decreased lipid accumulation and uptake in females.


Assuntos
Arsenitos/toxicidade , Metabolismo dos Lipídeos/efeitos dos fármacos , Cirrose Hepática/induzido quimicamente , Proteoma/genética , Caracteres Sexuais , Compostos de Sódio/toxicidade , Poluentes Químicos da Água/toxicidade , Peixe-Zebra/metabolismo , Animais , Arsenitos/farmacocinética , Relação Dose-Resposta a Droga , Feminino , Perfilação da Expressão Gênica , Immunoblotting , Metabolismo dos Lipídeos/genética , Cirrose Hepática/metabolismo , Masculino , Reação em Cadeia da Polimerase em Tempo Real , Compostos de Sódio/farmacocinética , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Transcriptoma , Poluentes Químicos da Água/farmacocinética
11.
Cell ; 149(2): 307-21, 2012 Apr 13.
Artigo em Inglês | MEDLINE | ID: mdl-22500798

RESUMO

Kinase inhibitors have limited success in cancer treatment because tumors circumvent their action. Using a quantitative proteomics approach, we assessed kinome activity in response to MEK inhibition in triple-negative breast cancer (TNBC) cells and genetically engineered mice (GEMMs). MEK inhibition caused acute ERK activity loss, resulting in rapid c-Myc degradation that induced expression and activation of several receptor tyrosine kinases (RTKs). RNAi knockdown of ERK or c-Myc mimicked RTK induction by MEK inhibitors, and prevention of proteasomal c-Myc degradation blocked kinome reprogramming. MEK inhibitor-induced RTK stimulation overcame MEK2 inhibition, but not MEK1 inhibition, reactivating ERK and producing drug resistance. The C3Tag GEMM for TNBC similarly induced RTKs in response to MEK inhibition. The inhibitor-induced RTK profile suggested a kinase inhibitor combination therapy that produced GEMM tumor apoptosis and regression where single agents were ineffective. This approach defines mechanisms of drug resistance, allowing rational design of combination therapies for cancer.


Assuntos
Neoplasias da Mama/tratamento farmacológico , Neoplasias da Mama/metabolismo , Resistencia a Medicamentos Antineoplásicos , MAP Quinase Quinase 1/antagonistas & inibidores , Proteínas Quinases/genética , Proteoma/análise , Animais , Antineoplásicos/uso terapêutico , Benzenossulfonatos/uso terapêutico , Benzimidazóis/uso terapêutico , Modelos Animais de Doenças , MAP Quinases Reguladas por Sinal Extracelular/antagonistas & inibidores , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Masculino , Camundongos , Niacinamida/análogos & derivados , Compostos de Fenilureia , Inibidores de Proteínas Quinases/uso terapêutico , Proteínas Quinases/metabolismo , Proteínas Proto-Oncogênicas c-myc/metabolismo , Piridinas/uso terapêutico , Receptores Proteína Tirosina Quinases/genética , Sorafenibe
12.
J Proteome Res ; 11(1): 279-91, 2012 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-21939285

RESUMO

Hemorrhage induced by snake venom metalloproteinases (SVMPs) is a complex phenomenon resulting in capillary disruption and blood extravasation. The mechanism of action of SVMPs has been investigated using various methodologies however the precise molecular events associated with microvessel disruption remains not fully understood. To gain insight into the hemorrhagic process, we analyzed the global effects of HF3, an extremely hemorrhagic SVMP from Bothrops jararaca, in the mouse skin and plasma. We report that in the HF3-treated skin there was evidence of degradation of extracellular matrix (collagens and proteoglycans), cytosolic, cytoskeleton, and plasma proteins. Furthermore, the data suggest that direct and indirect effects promoted by HF3 contributed to tissue injury as the activation of collagenases was detected in the HF3-treated skin. In the plasma analysis after depletion of the 20 most abundant proteins, fibronectin appeared as degraded by HF3. In contrast, some plasma proteinase inhibitors showed higher abundance compared to control skin and plasma. This is the first study to assess the complex in vivo effects of HF3 using high-throughput proteomic approaches, and the results underscore a scenario characterized by the interplay between the hydrolysis of intracellular, extracellular, and plasma proteins and the increase of plasma inhibitors in the hemorrhagic process.


Assuntos
Bothrops , Venenos de Crotalídeos/toxicidade , Hemorragia/sangue , Metaloproteases/toxicidade , Proteoma/metabolismo , Pele/metabolismo , Animais , Proteínas Sanguíneas/química , Proteínas Sanguíneas/metabolismo , Eletroforese em Gel Bidimensional , Hemorragia/induzido quimicamente , Masculino , Camundongos , Músculo Esquelético/efeitos dos fármacos , Músculo Esquelético/patologia , Fragmentos de Peptídeos/química , Mapeamento de Peptídeos , Proteólise , Proteoma/química , Pele/efeitos dos fármacos , Pele/patologia , Espectrometria de Massas em Tandem
13.
Semin Thromb Hemost ; 36(8): 845-56, 2010 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-21049385

RESUMO

All cell types shed ectosomes and exosomes, collectively known as microparticles (MP; 0.1 to 1.5 µm in diameter), when activated or stressed; normal human plasma contains ~2 µg MP protein/mL. The cellular composition of plasma MP is altered in many diseases, including acute coronary syndrome, diabetes mellitus, sepsis, and sickle cell disease. We measured the plasma MP protein composition of 42 patients (median age 69.5 years, most with cardiovascular disease) by label-free liquid chromatography coupled to tandem mass spectrometry. Among 458 proteins detected with high confidence (identified by at least two unique peptides with SEQUEST XCor (Thermo Electron Corp., San Jose, CA) ≥ 2.0, 2.2, and 3.3 for charge states +1, +2, and +3, respectively), 130 were present in most patients, representing a "core" set of plasma MP proteins. This core is enriched in cytoskeletal, integrin complex, and hemostasis proteins, and spectral counts of several proteins correlate with patient age and gender. We conclude that the MP proteome may be a useful and reliable source of biologically relevant disease biomarkers.


Assuntos
Micropartículas Derivadas de Células/química , Proteoma/análise , Fatores Etários , Idoso , Biomarcadores/análise , Cromatografia Líquida , Proteínas do Citoesqueleto , Hemostasia , Humanos , Integrinas , Proteínas/análise , Fatores Sexuais , Espectrometria de Massas em Tandem
14.
Clin Lab ; 54(3-4): 67-79, 2008.
Artigo em Inglês | MEDLINE | ID: mdl-18630736

RESUMO

The field of mass spectrometry-based proteomics has been transformed over the last decade due to advances in technology, sample preparation, bioinformatics, and computational tools. While this has led to a dramatic increase in research related to biomarker discovery, the promise of finding a significant number of new biomarkers has not yet materialized. Current proteomic technology is able to detect and analyze extremely small amounts of proteins (picomole to attomole level), but has difficulty detecting and quantifying proteins present at 2- to 3-orders of magnitude lower than the more abundant proteins. This is referred to as the dynamic range problem. Normal biological fluids used for biomarker discovery, such as plasma or urine, contain a small number of proteins present at much higher amounts than the remaining proteins. For example, in the plasma, albumin and immunoglobulins are present at milligrams per milliliter, while proteins of interest for biomarker discovery may be present at micrograms to picograms per ml. This has led us to investigate the microparticle subproteome which has a high likelihood of containing potential biomarkers. While this subproteome makes up less than 0.01% of the total plasma proteome, it is rich in proteins altered under a variety of pathological conditions.


Assuntos
Biomarcadores/sangue , Proteínas Sanguíneas/análise , Espectrometria de Massas/métodos , Plasma/química , Proteômica/métodos , Antígenos de Superfície/análise , Humanos , Microquímica/métodos , Vesículas Secretórias/química
15.
J Proteome Res ; 7(5): 2088-96, 2008 May.
Artigo em Inglês | MEDLINE | ID: mdl-18373357

RESUMO

Bladder cancer leads to approximately 13,000 deaths annually in the United States. Early disease is often treated with minimal morbidity and has good prognosis, while the opposite is true for advanced disease. Currently, no tools exist for early detection of this cancer. Microparticles are small, subcellular particles released by essentially all cells upon activation and are known to be produced constitutively by cancer cells. Since most bladder cancers originate in the urothelial cells lining the lumen of the organ, we hypothesize that these cells will release microparticles into the urine. The goal of this study was to identify potential biomarkers in the urinary microparticles of individuals with bladder cancer. Urine microparticles from five healthy individuals and four individuals with bladder cancer were isolated. Samples were delipidated by PAGE and trypsin-digested, peptides were extracted, and the proteome was examined by LC-MS/MS using a Thermo Finnigan LTQ and LTQ-FT ion trap mass spectrometer. Protein identification was determined by SEQUEST and relative quantitation was assessed by comparing spectral counts. Eight proteins were elevated in the microparticles from individuals with bladder cancer. They include five proteins associated with the epidermal growth factor receptor pathway, the alpha subunit of GsGTP binding protein, resistin, and retinoic acid-induced protein 3. Further studies will be needed to validate these potential biomarkers.


Assuntos
Biomarcadores Tumorais/análise , Proteoma/análise , Neoplasias da Bexiga Urinária/química , Urina/química , Idoso , Feminino , Hematúria , Humanos , Masculino , Pessoa de Meia-Idade , Dados de Sequência Molecular , Distribuição Aleatória , Reprodutibilidade dos Testes , Neoplasias da Bexiga Urinária/metabolismo
16.
Proteomics ; 7(20): 3681-92, 2007 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-17879999

RESUMO

LC-MS/MS with certain labeling techniques such as isotope-coded affinity tag (ICAT) enables quantitative analysis of paired protein samples. However, current identification and quantification of differentially expressed peptides (and proteins) are not reliable for large proteomics screening of complex biological samples. The number of replicates is often limited because of the high cost of experiments and the limited supply of samples. Traditionally, a simple fold change cutoff is used, which results in a high rate of false positives. Standard statistical methods such as the two-sample t-test are unreliable and severely underpowered due to high variability in LC-MS/MS data, especially when only a small number of replicates are available. Using an advanced error pooling technique, we propose a novel statistical method that can reliably identify differentially expressed proteins while maintaining a high sensitivity, particularly with a small number of replicates. The proposed method was applied both to an extensive simulation study and a proteomics comparison between microparticles (MPs) generated from platelet (platelet MPs) and MPs isolated from plasma (plasma MPs). In these studies, we show a significant improvement of our statistical analysis in the identification of proteins that are differentially expressed but not detected by other statistical methods. In particular, several important proteins - two peptides for beta-globin and three peptides for von Willebrand Factor (vWF) - were identified with very small false discovery rates (FDRs) by our method, while none was significant when other conventional methods were used. These proteins have been reported with their important roles in microparticles in human blood cells: vWF is a platelet and endothelial cell product that binds to P-selectin, GP1b, and GP IIb/IIIa, and beta-globin is one of the peptides of hemoglobin involved in the transportation of oxygen by red blood cells.


Assuntos
Cromatografia Líquida/estatística & dados numéricos , Peptídeos/análise , Peptídeos/classificação , Coloração e Rotulagem/estatística & dados numéricos , Espectrometria de Massas em Tandem/estatística & dados numéricos , Cromatografia Líquida/métodos , Biologia Computacional/métodos , Biologia Computacional/estatística & dados numéricos , Humanos , Marcação por Isótopo/métodos , Marcação por Isótopo/estatística & dados numéricos , Proteômica/métodos , Proteômica/estatística & dados numéricos , Coloração e Rotulagem/métodos , Espectrometria de Massas em Tandem/métodos
17.
Thromb Haemost ; 97(1): 67-80, 2007 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-17200773

RESUMO

Microparticles (MPs) are small membrane vesicles generated by essentially all cell types. In the plasma, most MPs are derived from platelets, but those from other sources, particularly leukocytes (macrophages, lymphocytes, and neutrophils), endothelial cells, and even smooth muscle cells can be detected and appear to play an important role in normal physiology and various diseases. In previous work we analyzed the proteome of MPs generated from isolated platelets (platelet MPs). Here, we report on a comparative analysis of microparticles isolated from plasma (plasma MPs) versus platelet MP using two complementary methods of comparative analysis. The first method, spectral count analysis, yielded 21 proteins detected in plasma MPs (with a total spectral count of 10 or greater) that were essentially absent in platelet MPs (with a total spectral count of 1 or 0). An additional two proteins (von Willebrand Factor, albumin) were present in both types of MPs but enriched in the plasma MPs. The second method, isotope-coded affinity tag (ICAT) labeling of proteins, supported the spectral count results for the more abundant proteins and provided better relative quantitation of differentially expressed proteins. Proteins present only in the plasma MPs include several associated with apoptosis (CD5-like antigen, galectin 3 binding protein, several complement components), iron transport (transferrin, transferrin receptor, haptoglobin), immune response (complement components, immunoglobulin J and kappa chains), and the coagulation process (protein S, coagulation factor VIII).


Assuntos
Plaquetas/química , Plasma/química , Proteínas/análise , Proteômica/métodos , Apoptose , Coagulação Sanguínea , Membrana Celular/química , Humanos , Imunidade , Ferro/metabolismo , Tamanho da Partícula
18.
J Proteome Res ; 4(5): 1516-21, 2005.
Artigo em Inglês | MEDLINE | ID: mdl-16212402

RESUMO

Platelet-derived microparticles are the most abundant type of microparticle in human blood and contribute to many biologically significant processes. Here, we report the first proteomic analysis of microparticles generated from activated platelets. Using 1D SDS-PAGE and liquid chromatography coupled to a linear ion trap mass spectrometer, the identification of 578 proteins was accomplished using a minimum of 5 MS/MS detections of at least two different peptides for each protein. These microparticles displayed many proteins intrinsic to and well-characterized on platelets. For example, microparticles in these experiments were found to contain membrane surface proteins including GPIIIa, GPIIb, and P-selectin, as well other platelet proteins such as the chemokines CXCL4, CXCL7, and CCL5. In addition, approximately 380 of the proteins identified were not found in two previous studies of the platelet proteome. Since several of the proteins detected here have been previously implicated in microparticle formation and/or pathological function, it is hoped that this study will help fuel future work concerning the possible role of microparticles in various disease states.


Assuntos
Plaquetas/metabolismo , Proteômica/métodos , Animais , Separação Celular , Quimiocina CCL5 , Quimiocinas CC/química , Cromatografia Líquida , Eletroforese em Gel de Poliacrilamida , Citometria de Fluxo , Humanos , Integrina beta3/química , Espectrometria de Massas , Selectina-P/química , Peptídeos/química , Agregação Plaquetária , Fator Plaquetário 4/química , Complexo Glicoproteico GPIb-IX de Plaquetas/química , Glicoproteínas da Membrana de Plaquetas/química , Proteoma , beta-Tromboglobulina
19.
Shock ; 18(5): 423-7, 2002 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-12412620

RESUMO

The generation of oxygen radicals during leukocyte-endothelial cell interaction is considered to represent one of the fundamental steps of microvascular injury following ischemia and reperfusion. Indirect evidence also suggests that this relationship may be important following hemorrhagic shock. The purpose of this study was to characterize the temporal changes of reactive oxygen species (ROS) in the mesenteric microvascular endothelium, in vivo, as a consequence of hemorrhagic shock and reperfusion, and to correlate this ROS production to leukocyte adherence. Following a control period, blood was withdrawn to reduce the mean arterial pressure to 40 mmHg for 1 h in urethane-anesthetized rats. Mesenteric venules in a transilluminated segment of small intestine were examined to quantitate changes in ROS generation and leukocyte adherence. Sprague-Dawley rats were injected with dihydrorhodamine 123, a hydroperoxide-sensitive fluorescent probe that is trapped within viable cells as a nonfluorescent form and then converted to the mitochondrion-selective form rhodamine 123 by hydroperoxides. The fluorescent light emission from rhodamine 123 was recorded with digital microscopy and downloaded to a computerized image analysis program. Our results demonstrated an 80% increase in ROS generation beginning within 5 min into resuscitation and a 10-fold increase in leukocyte adherence that occurred at 10 min after resuscitation. Both ROS generation and leukocyte adherence were attenuated with pre-shock administration of platelet activating factor (PAF) antagonist, WEB 2086, and the CD11/CD18a antibody, anti-LFA-1beta. Our findings suggest that ROS production in endothelial cells is increased during reperfusion following hemorrhagic shock and that the mechanism of expression is mediated in part by both PAF expression and subsequent leukocyte adherence.


Assuntos
Endotélio Vascular/patologia , Leucócitos/patologia , Espécies Reativas de Oxigênio/metabolismo , Choque Hemorrágico/metabolismo , Choque Hemorrágico/patologia , Animais , Azepinas/farmacologia , Adesão Celular , Corantes Fluorescentes , Antígeno-1 Associado à Função Linfocitária/fisiologia , Masculino , Microcirculação/lesões , Microcirculação/metabolismo , Microcirculação/patologia , Fator de Ativação de Plaquetas/antagonistas & inibidores , Ratos , Ratos Sprague-Dawley , Traumatismo por Reperfusão/metabolismo , Traumatismo por Reperfusão/patologia , Ressuscitação , Rodaminas , Triazóis/farmacologia
20.
Free Radic Biol Med ; 33(1): 52-62, 2002 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-12086682

RESUMO

Although native LDL (n-LDL) is well recognized for inducing endothelial cell (EC) dysfunction, the mechanisms remain unclear. One hypothesis is n-LDL increases caveolin-1 (Cav-1), which decreases nitric oxide (*NO) production by binding endothelial nitric oxide synthase (eNOS) in an inactive state. Another is n-LDL increases superoxide anion (O(2)(*-)), which inactivates *NO. To test these hypotheses, EC were incubated with n-LDL and then analyzed for *NO, O(2)(*-), phospho-eNOS (S1179), eNOS, Cav-1, calmodulin (CaM), and heat shock protein 90 (hsp90). n-LDL increased NOx by more than 4-fold while having little effect on A23187-stimulated nitrite production. In contrast, n-LDL decreased cGMP under basal and A23187-stimulated conditions and increased O(2)(*-) by a mechanism that could be inhibited by L-nitroargininemethylester (L-NAME) and BAPTA/AM. n-LDL increased phospho-eNOS by 149%, eNOS by approximately 34%, and Cav-1 by 28%, and decreased the association of hsp90 with eNOS by 49%. n-LDL did not appear to alter eNOS distribution between membrane fractions (approximately 85%) and cytosol (approximately 15%). Only 3-6% of eNOS in membrane fractions was associated with Cav-1. These data support the hypothesis that n-LDL increases O(2)(*-), which scavenges *NO, and suggest that n-LDL uncouples eNOS activity by decreasing the association of hsp90 as an initial step in signaling eNOS to generate O(2)(*-).


Assuntos
Caveolinas/metabolismo , Ácido Egtázico/análogos & derivados , Endotélio Vascular/efeitos dos fármacos , Proteínas de Choque Térmico HSP90/metabolismo , Lipoproteínas LDL/farmacologia , Óxido Nítrico Sintase/metabolismo , Animais , Transporte Biológico , Western Blotting , Calmodulina/metabolismo , Bovinos , Caveolina 1 , Células Cultivadas , Quelantes/farmacologia , GMP Cíclico/metabolismo , Ácido Egtázico/farmacologia , Endotélio Vascular/enzimologia , Ativação Enzimática , Inibidores Enzimáticos/farmacologia , Humanos , NG-Nitroarginina Metil Éster/farmacologia , Óxido Nítrico/metabolismo , Óxido Nítrico Sintase/antagonistas & inibidores , Óxido Nítrico Sintase Tipo III , Nitritos/metabolismo , Fosforilação , Superóxidos/metabolismo
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